› 5d3s

X-ray diffraction
1.75Å resolution

First bromodomain of BRD4 bound to inhibitor XD44

Released:
DOI: 10.2210/pdb5d3s/pdb
PDB entry 5d3s coloured by chain, front view.
PDB entry 5d3s coloured by chain, side view.
PDB entry 5d3s coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1).
Hügle M, Lucas X, Weitzel G, Ostrovskyi D, Breit B, Gerhardt S, Einsle O, Günther S, Wohlwend D
J Med Chem 59 1518-30 (2016)
PMID: 26731611

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130112 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bromodomain-containing protein 4 Chain: A
Molecule details ›
Chain: A
Length: 126 amino acids
Theoretical weight: 15.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60885 (Residues: 44-168; Coverage: 9%)
Gene names: BRD4, HUNK1
Sequence domains: Bromodomain
Structure domains: Bromodomain-like

Ligands and Environments

3 bound ligands:
Ligand 579 1 x 579
Ligand DMS 1 x DMS
Ligand BU3 1 x BU3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 39.48Å b: 49.51Å c: 57.79Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.195
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Drug Discovery Targeting Bromodomain-Containing Protein 4.
Liu et al. (2017)
5 more

2 mentions without citation

The role of loop dynamics in the prediction of ligand-protein binding enthalpy.
Çınaroğlu et al. (2023)
1 more